EMBOSS: ednapars

ednapars

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Function

Conversion of PHYLIP's dnapars

Description

EDNAPARS -- Embossified DNA Parsimony Program

Phylip dnapars documentation.

Usage

Here is a sample session with ednapars using test data:-

   5   13
Alpha     AACGUGGCCAAAU
Beta      AAGGUCGCCAAAC
Gamma     CAUUUCGUCACAA
Delta     GGUAUUUCGGCCU
Epsilon   GGGAUCUCGGCCC


% ednapars test 

DNA parsimony algorithm
Output file [ednapars.outfile]: stdout
Randomize input order of species [N]: 
Create a tree file [Y]: 
Output treefile name [ednapars.treefile]: 

One most parsimonious tree found:



           +--Epsilon   
        +--4  
     +--3  +--Delta     
     !  !  
  +--2  +-----Gamma     
  !  !  
--1  +--------Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


requires a total of     19.000




% more more ednapars.treefile
((((Epsilon,Delta),Gamma),Beta),Alpha);

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-msf]               seqset     File containing a sequence allignment
  [-outfile]           outfile    Output file name
*  -random             bool       Randomize input order of species
*  -randseed           integer    Random number seed (must be odd)
*  -randtimes          integer    How many times to randomise
*  -outgnum            integer    number of the outgroup
*  -valthresh          float      threshold value
  [-[no]trout]         bool       Create a tree file
*  -treefile           outfile    Tree file name

   Optional qualifiers:
   -[no]besttree       bool       Search for best tree
   -og                 bool       Outgroup root
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -steps              bool       Print out steps in each site
   -seqatnodes         bool       Print sequences at all nodes of tree
   -[no]drawtree       bool       Draw tree

   Advanced qualifiers:
   -thresh             bool       Use Threshold parsimony

Mandatory qualifiers Allowed values Default

[-msf]
(Parameter 1) File containing a sequence allignment Readable sequences Required

[-outfile]
(Parameter 2) Output file name Output file ednapars.outfile

-random Randomize input order of species Yes/No No

-randseed Random number seed (must be odd) Any integer value 3

-randtimes How many times to randomise Any integer value 3

-outgnum number of the outgroup Integer 1 or more 1

-valthresh threshold value Number 1.000 or more 1.0

[-[no]trout]
(Parameter 3) Create a tree file Yes/No Yes

-treefile Tree file name Output file ednapars.treefile

Optional qualifiers Allowed values Default

-[no]besttree Search for best tree Yes/No Yes

-og Outgroup root Yes/No No

-printdata Print out the data at start of run Yes/No No

-progress Print indications of progress of run Yes/No No

-steps Print out steps in each site Yes/No No

-seqatnodes Print sequences at all nodes of tree Yes/No No

-[no]drawtree Draw tree Yes/No Yes

Advanced qualifiers Allowed values Default

-thresh Use Threshold parsimony Yes/No No

Mandatory qualifiers	Allowed values	Default
[-msf] (Parameter 1)	File containing a sequence allignment	Readable sequences	Required
[-outfile] (Parameter 2)	Output file name	Output file	ednapars.outfile
-random	Randomize input order of species	Yes/No	No
-randseed	Random number seed (must be odd)	Any integer value	3
-randtimes	How many times to randomise	Any integer value	3
-outgnum	number of the outgroup	Integer 1 or more	1
-valthresh	threshold value	Number 1.000 or more	1.0
[-[no]trout] (Parameter 3)	Create a tree file	Yes/No	Yes
-treefile	Tree file name	Output file	ednapars.treefile
Optional qualifiers	Allowed values	Default
-[no]besttree	Search for best tree	Yes/No	Yes
-og	Outgroup root	Yes/No	No
-printdata	Print out the data at start of run	Yes/No	No
-progress	Print indications of progress of run	Yes/No	No
-steps	Print out steps in each site	Yes/No	No
-seqatnodes	Print sequences at all nodes of tree	Yes/No	No
-[no]drawtree	Draw tree	Yes/No	Yes
Advanced qualifiers	Allowed values	Default
-thresh	Use Threshold parsimony	Yes/No	No

Data files

Notes

Multiple sequences sets not implemented yet!.

References

Warnings

Diagnostics

Exit status

Known bugs

Author(s)

(c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.